It is estimated the reform, including the amnesty, will generate more than $830 million and stimulate the ailing economy.
Noboa took office last month promising to improve economic conditions, especially for youth, amid surging crime in the Andean country.
The reform was approved by 107 legislators out of 135 present in the session, with minor changes that the 36-year-old president can now approve or reject.
"We will once again have order and the resources to combat lawlessness," said Noboa in a statement after the vote.
The new tax incentives, mostly in the form of income tax discounts, will apply to companies that hire workers aged 18-29 for a minimum of one year.
Last week, Noboa told Reuters in an interview that he expects the incentives to cut youth unemployment by at least 10 percentage from its current rate which exceeds 50%.
The tax amnesty offers a waiver on interest due on outstanding tax debts, as well as fines. It does not allow officials like the wealthy Noboa, their relatives or lawmakers to file for the benefit.
The business of Noboa's father, banana magnate Alvaro Noboa, owes more than $89 million in delinquent taxes, according to Ecuador's tax authority.
In addition to the amnesty, the reform includes monthly income tax payments for the largest taxpayers, as well as a refund on sales taxes paid for purchases of construction materials and some real estate developments, in a bid to attract more private investment.
(Reporting by Alexandra Valencia; Writing by David Alire Garcia; Editing by David Gregorio)
